Whatever's Left
by SleepingThroughTime
Summary: (Read my other story, 'Passings' before you read this, I know I suck at summaries. M for language and distressing subjects.) After a near death experience and the loss of her first child, how will Jane cope when Khan makes an alliance with the Klingon Empire?
1. Chapter 1

**Well, I know it has been ages and I promised a sequel, I just hadn't had much time, I still kinda don't and updates will be infrequent until summer.**

**If you haven't read my last story, I think I dragged that out too long, I could have made it shorter, anyways, read that before you read this, beware of horrible mistakes I had forgotten to correct, hopefully there won't be as many in this one.**

**Anyways, here we go.**

* * *

Khan stared at her through the frosted glass; she was paler now, much paler. Her chestnut coloured hair flowed around her rounded face.

She looked peaceful.

She looked dead.

He couldn't quite believe how much he had hated her back in the Archive, he hated that she never spoke. It was like pulling teeth trying to have a conversation with her. Then things changed, he was more interested when he knew what her interests were.

Tracing a finger around the glass, he could make out the small details of her face, the birth mark on her neck and the contours of her collar bone.

He wished he never dragged her into this mess, she wouldn't be half dead, and they wouldn't have a dead child. Yet, at the same time, he could never let her go; he could never bear to see her in another man's arms. He would kill anyone who would try and steal her away.

But deep down, he knew she would never end up with another man if she never worked in the Archive and met him. She was so awkward, she shied away from men, and he sensed fear from this. Probably from her size and the fear of being hurt by other men.

"Sir?" a voice interrupted his thoughts.

"I said no one was to enter this room unless I saw it fit." his voice was threatening.

He heard steps near his position; he spun around, his eyes glaring. "I said leave!" he yelled.

Anika sighed and stared up. "I have news."

"Couldn't you have used the comm system?" he snapped as he moved closer.

"I have news about her." Anika didn't seem threatened from him at all, she knew Khan all of her life, she knew he wouldn't harm her unless there was reason to.

Khan froze in his tracks, staring directly into her large brown eyes.

"I've came up with a way of repairing her wound, but it's risky, it may damage her spine and leave her paralysed." Anika said slowly and softly, knowing how much she meant.

Gulping, Khan looked slowly away. He couldn't have her paralysed. He couldn't have her disabled.

He was a part of a group of men and woman who are opposed to anything less than perfect. Even though he wasn't as harsh an augment leader compared to others back two hundred years ago, there was no slavery or massacres in the territory he had claimed, in the eyes of some of his followers he would look weak.

"Can you help her if that would happen?" his voice was quiet as he looked at her again.

Anika sighed and shrugged. "Over time, yes, she would be able to walk again, but with time and a great deal of help."

Khan looked away once more; silence filled the room for what seemed like a thousand years for Anika.

"When can you perform the procedure?" Khan moved back to the cryotube, his eyes concentrated on Jane.

Anika stayed where she was, her hands joined behind her back. "Tomorrow afternoon. I don't quite know how long it'll take."

"Do it then."

* * *

James Kirk was in Starfleet Medical, laying on a biobed with hospital garments covering him. It had been a week since he was rescued, being back and free to move around felt... Strange.

He couldn't deny it didn't after months of being imprisoned and beaten day after day. It drove him slowly mad, then without really thinking like he normally did, he shot a pregnant former crewmen dead.

Even if she was with Khan, it was wrong; he could now admit that as he slowly regained his sanity. He regretted the moment he put pressure on the trigger of that phaser rifle, but there was no going back now.

Jim sat up a little on his bed; most of his wounds were now healed. He stared at the door, waiting for his daily visit from Bones.

The grumpy doctor made an appearance each day a little after noon; he often came with decent food for his friend, knowing what food in the place was like.

"Afternoon," Leonard mumbled as he walked in. "Good news is you're getting discharged tomorrow, bad news is you're not allowed to resume command for two months, Spock's in charge until your mental health is back to the way it was."

Jim nodded at his words. "I'm allowed on the ship?"

Bones sighed and shrugged. "I don't see why not, but no work." he mumbled as he moved to sit next to the bed, handing Jim a plastic box of heated chilli he had made the night before.

Jim opened it, taking a fork he saved from his last meal. "You'd make an excellent chef, you know?"

Bones rolled his eyes. "Glad to know."

Jim chucked just a little then sighed. "How is she?"

"Who?" Bones questioned. "The Enterprise?"

Jim nodded slowly as he took a mouthful of food.

"Repairs are done, there was a systems update, and everything looks as good as new." Bones reported, fidgeting a little. "Command wants us to patrol the Klingon neutral zone; they seem to think we'll find the homicidal maniac there."

Jim looked over once he devoured everything in the box. "When do you leave?"

"Two weeks from tomorrow."

"Mind if I tag along?"

Bones grinned. "I don't see why not."

* * *

Jane was taken from the cryotube a little after noon. Khan watched everything, he wanted to reach out and touch her, to hold her, but he'd have to wait.

She was kept under a sedative while Anika started the procedure; he stood by her side, assisting where he could.  
About four hours later they finished, a blanket was laid over her. Khan sat by her, he moved to take her hand, which was much smaller compared to his. Pale and bony. He enveloped it with both of his, heating it slowly.

Anika sighed at the sight, she never saw him so affectionate towards a woman. She never saw him truly love a woman. She had, however, seen him use women. Sometimes for a simple fuck, other times to actually obtain information. She found it hard to believe he was capable of loving after all he had did.

"Her vitals seem fine." she said softly.

Khan nodded slowly. "Can you wake her?"

Anika sighed. "She would be to exhausted too stay up long, but yes, I can."

After pressing a hypospray against her neck, Jane slowly woke, her vision blurred.

Khan clutched her hand tightly, yet not tight enough to hurt her.

Jane turned her head slowly, knowing Khan was there from the grip. Her head was thumping, her mouth was dry, she wasn't sure how long she would be able to stay awake, but she had a question on the tip of her tongue. "Is... the baby al-alright?" she managed to get out, it was little over a whisper.

Khan stared at her, unable to answer. He didn't know how. For the first time in his life he couldn't answer a question, this was a man who understood complex mathematics by the time he was seven.

By the time he managed to open his mouth, she fell back to sleep.


	2. Chapter 2

**Hey, back with another chapter. I depressed myself while writing and I was close to crying at times so I tried to balance it by returning to the crew of the Enterprise.****Enjoy and make sure to leave a review.**

* * *

Feeling drowsy, Jane slowly began to open her heavy eyes; they stung for a moment, almost as if she had soap in her eyes. The sensation quickly disappeared after she blinked a couple of times, her vision was slightly blurred, she saw a dark figure looming over her in the otherwise brightly lit room. She could tell she was in sickbay by the smell lingering in the air, the same sterilized smell that was present in ever sickbay or hospital. Her legs felt numb, as if she was given anaesthetics from her back down. She tried to move them a little, but it resulted in pain. She winced at the feeling as her eye sight sharpened. The dark figure turned out to be Khan, his expression was soft as he held her hand, tracing random shapes on the palm of her hand.

"Don't try to move." he said softly as he moved some hair from her face.

Jane rolled her eyes and stretched her stiff free arm, and then she moved it to rest on her stomach.

It was flat.

It wasn't meant to be flat.

With wide eyes she looked at Khan panicked. "What happened? Where is he?!"

Khan gulped, and that was an indication to her that something was terribly wrong.

She should have never left their quarters for that walk.

Anika moved by Khan as she ran her tricorder over her. "Her legs are fine, she won't be able to move much on them without being in pain for about a fortnight." she informed him and he nodded as response.

"Where's my baby?" Jane asked quickly, hating they were avoiding answering the question.

Anika looked at Khan for a brief moment then at her. "You were shot by our prisoners, the shock of it all was too much for him." she said slowly, her expression soft like Khan's.

Jane froze her face blank as she tilted her head slowly towards Khan. _This wasn't happening. He wasn't dead, this was some sort of cruel joke they were playing on her. Was it the first of April? Please may it be that._

But when she saw Khan's eyes she knew it wasn't a joke, they looked like he was holding hurt inside, she could read him through his eyes. He'd never admit things like that or show it on his face, she just knew.

She quickly knew it wasn't Scotty that shot her, no, he would never hurt her, he still believed they were friends; he cared too much for her.

Carol Marcus was an uncertain candidate, even though Khan killed her father right in front of her.

Then there was Jim Kirk. The man Khan was slowly driving insane from daily beatings.

"Who shot me?" Jane's voice was only a little over a whisper.

Khan clenched his jaw as he stared into her dark blue eyes, seeing the hurt there. What woman wouldn't be hurt if her child was taken from her?

"James Kirk."

Jane kept staring, frozen. No tear fell from her eyes. This worried him, why was she not reacting? This made absolutely no sense.

* * *

Jim stood with a suitcase with the bare essentials in one hand, dressed in civilian clothing which consisted of a pair of jeans, a pain grey top and a black leather jacket while he waited for Bones outside the Starfleet Medical buildings. He was discharged not long before then, maybe just an hour before. He now stood in the summer sun shine in the otherwise cold city of San Francisco. Nearby leaves rustled from the gentle sea breeze coming off the bay, which was not far away from where he stood.

A group of young nurses passed him in the usual short uniform, all giggling amongst each other. Yet he said nothing to them, he didn't maintain a stare with them. He had changed and Bones had noticed.

The man had walked towards his friend slowly. Jim was completely different after being saved from that bastard. He looked at women differently. He didn't try to flirt with them, nor did he constantly stare at their backsides, chest or legs as frequently. Of course he still did, but it was strange. This was Jim. Leonard first noticed this with the young nurse who cared for him while in hospital, he made no move to flirt. Leonard then came to the conclusion that this was because of two reasons;

First reason being that Jim had lost complete interest in women and was now gay. He found himself laughing at that. He couldn't begin to imagine that.

Second reason being that he had found a woman he really liked. Leonard found himself believing this one because of one reason. The constant jabbering about a certain Carol Marcus.

'How's Miss Marcus?' and 'How's Carol doing?' were constant questions whenever he gave a visit to him.

Leonard smirked to himself at the thoughts that old perfect hair found someone that he may maintain a relationship with.

"Hey Bones." Jim smiled weakly at him.

"How you feeling today?" the gruff voiced doctor asked.

"Better. Is Carol now on the Enterprise like I asked?" Jim asked as he began to walk along.

"For the twelfth time yes! Why do you keep asking?" he questioned.

"Curious." he rolled his eyes as they began to make their way to the shuttle bay to catch the last shuttle leaving for the Enterprise, which was now shiny and new up in space dock.

* * *

Khan held Jane in his arms after he was given permission to move her. He moved through the dark deck towards their quarters. He was scarcely in there while she was cryogenically frozen for what seemed like years to him. He felt her clutching his tight fitting shirt; her face was buried into his chest. He found himself worrying more; she had yet to make a response to what had just happened.

He entered their rooms and moved slowly to the bedroom, setting her down carefully as he pressed a hypospray against her neck for an extra dose of pain relief. She remained staring off into the bulkhead.

He sat on the edge of the bed; it dipped down beneath his weight as he rested a large hand on her waist, running it up and down her side. "You should shower." he whispered.

He didn't get a response.

He sighed and decided to take it upon himself to wash her so he lifted her carefully and moved the bathroom, turning on a shower. "We can't use the bath as we're short on water," he explained. "We've found an M class planet, I'm going on away mission to retrieve water tomorrow." he sighed as he leaned her against the sink so he could undress. She watched, but only his face. "I won't go if you wish me to stay."

No response.

Khan sighed once more as he saw she wasn't going to undress herself anytime soon so started for her.

"Can you stand for long?" he asked as he knelt down to help her rid her feet of her trousers. He looked up as she gave a small shake of her head.

Finally some form of communication.

He stood back up to his normal height and picked her up, wrapping her legs around his waist while she wrapped her arms around his neck.

"Is that better than standing?" he asked as he watched her.

She gave a small nod.

With that nodded he moved into the shower with her clinging onto him. He set the temperature so there would be some steam, yet it wasn't hot enough to scold her. He let the spray of water fall over them both, making sure her hair was thoroughly soaked before he took shampoo to wash it.

Jane kept her head down as his fingers worked through her hair and massaged her scalp. She looked down at her flat stomach then noticed something that wasn't there before. A scar beneath her belly button. He must have been taken from her there.

She then burst out in tears as she stared at the place where her little boy was taken.

* * *

Jim sighed as he nodded at some crewmen as he walked through the brightly lit decks of his ship towards the turbolift, still in civilian clothing. Well, it was Spock's ship for the time being, he wasn't permitted to resume command for an entire month, but he found that he didn't mind, all he cared about was being back on the ship.

After the short trip by turbolift he found himself on the bridge, grinning widely.

"Captain!" Uhura exclaimed as she was about to walk past him, everyone then turned their heads to him.

Spock was comfortably giving commands from the captain's chair before he stood immediately and turned. "Ji- Captain, we did not expect you back so soon." a hint of surprise in his otherwise emotionless voice.

"Well, Command is letting me stay on board until I'm cleared for duty," he explained. "I'll just be observing really."

Spock nodded as he finished explaining. "It is good to see you well again."

Jim smiled at his Vulcan friend before he turned and began giving commands again. "Mr Sulu, take us out of space dock."

Hikaru looked around a smiled at Jim for a brief moment before he responded. "Aye, commander."

"I'm glad to see you're fine." Uhura beamed as she moved passed him.

As they prepared the jump to warp Jim wandered to a certain woman's station. "I see you're better."

Carol chuckled. "I wasn't injured."

Jim nodded and leaned against the station. "What time does your shift end?"

Carol raised a brow. "1800, why?"

Jim shrugged. "I have a few zombie movies from the early twenty-first century I've been meaning to watch. Was also thinking of something Italian for dinner." he smiled.

Carol nodded and smiled. "I'll be there."

**Leave a review with your thoughts!**


	3. Chapter 3

**Sorry for the lack of activity the past month. I've just been busy with exams and stuff, it sucks.****Anyway, leave a review on what you think of this chapter :) Also, this contains information on Khan's past, here's the link if you want to check it out.**** wiki/Khan_Noonien_Singh_(alternate_reality)**

Wrapped in a soft blanket as she lay in bed, Jane stared off. Her eyes were still puffy and red from the crying. She felt the bed shift beneath a weight behind her, and then an arm slid protectively around her middle as long, bony fingers brushed a few strands of hair away. She couldn't believe anything that was happening around her. It didn't feel real. You always would hear about horrible things happen to other people, yet you would never think it would happen to you. Now here she was depressed. She wasn't sure how long this would last for, she was like this before as a teenager as pressure from her dad and school. If only she knew things improved after that, it would have helped.

Arms were slowly wrapped around her, he small body pulled against his large one as his chin settled on her head, breathing in the scent of her freshly washed hair. She relaxed under his hold, feeling safe and protected. He took care of her the entire evening, showering her, drying her hair, dressing her. She felt like a child again when her dad would dry her hair and braid it. He was talented for a dad. She felt she should be thankful. She was always thankful to him, having saved her from being raped by that man the night he escaped from the Archive, and from being killed by Marcus.

"We're going to Kronos after we stopped tomorrow." he broke the silence with a soft voice.

Jane slowly turned to face him, sniffling a little. "Why?" her voice was only a little over a whisper.

Khan sighed and stroked her hair softly. "I'll explain later," he whispered. "Sleep."

The puzzled look on Jane's face remained as she rested her head on his chest, slowly falling into a much needed deep sleep.

* * *

Jim laid in bed the next day smiling to himself. The previous night had been a pleasant one. It began with a small meal then was followed by a film along with a few kisses scattered here and there while curled up on the small sofa he managed to have in his quarters. They were due to have another date tonight. He planned not to mess this up with Carol like he did with plenty of woman before her.

Standing up he peered into the nearby mirror, glad to see scars healing. They would always be there though, visual reminders of what he endured during those long months of being treated like an animal. He pulled on a shirt and was about to read up in something before there was a knock on the door.

"Enter." Jim called out.

Bones popped his head through, looking like he was in a rush. "You better get up to the bridge."

Before he could ask why he noticed the ship had went to yellow alert. "On my way." he mumbled as he hurried out.

* * *

Jane woke up early the next morning, her eyes were stinging. She then realised she had cried during the night. She looked up to discover Khan was awake and watching over her. Sighing, she cuddled back into him. "You should go on that away mission," she whispered. "I'll be fine."

"You won't." he whispered in return.

"Everybody else needs you."

"Joachim is in charge, we've known each other since we were children, they'll be fine."

Jane sighed and looked up at him. "You never spoke about your childhood."

"Well, I was born in 1970, genetically enhanced as an embryo before being placed in my mother, Sarina Kaur. She was the director of the Chrysalis project. Everybody on this ship apart from you was created in that project." he answered with a sigh while Jane listened intently.

"When I was a year old an accident happened and as a result I lost a leg."

"What? Seriously?"

Khan nodded. "My mother then abandoned me on the streets of New Delhi, there I met Joachim. He protected me when I couldn't until we were taken in by Dr. Heisen as part as his Eugenics Project." Jane noticed his jaw clench. "He gave me my leg and we endured seven years of mental and physical training, he kept us in check with neural inhibitors." his grip on her tightened. "I crushed his skull when I was fifteen."

Jane was frowning before she hugged him close.

Khan shut his eyes, caressing her back gently. "I'm going to negotiate with the Klingons."

The puzzled look on her face returned as she looked up.

"I will give them advanced technology to defeat the Federation, and in turn I get Earth."

* * *

"A Romulan Warbird?" Jim looked puzzled as he looked at the view screen. "Why is it all the way out here?"

"Uncertain." Spock answered as he turned to look back at the warbird. "We received the distress call seven hours ago, we arrived only minutes ago."

Jim moved across the bridge. "Life signs."

"None. We should board and look for survivors." Sulu answered.

"I'll lead an away team." Jim volunteered, desperate for action.

Spock approved. "Any other volunteers?"

Chekov and a few others, including Carol decided to raise their hands in order to volunteer.

Jim looked at them all. "We leave in an hour."

**Sorry for the length of this, next chapter will be longer, promise.**


End file.
